Diplomacy is so much a part of war that it can't take a back seat regardless of if we are talking only about Minors or majors.
Things like that only happen because the game continues to treat the AI and players exactly the same. Just because you give the player more tools to influence the tides of the game by means of diplomacy doesn't mean you have to give the AI the exact same tools. No, an AI controlled Switzerland should not be joining the Allies in 1939. But a player controlled Switzerland shouldn't be held to that same limitation.
The hole in the argument is that the AI and humans will continue to be treated the same. PI has never said that it would do otherwise.
Oh and based on your logic a human USA should be able to join SU or Germany right? Or have a human France leave the allies and join Germany and attack UK.